Dear All: I want to find the WM lobar volumes in a set of MS patients. I also have the processed images from freesurfer. To extract the lobar volumes I used below codes from one of the previous threads of Freesurfer (https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-April/023232.html):
1. mri_annotation2label --s <sub1> --hemi rh --lobesStrict lobesfile 2. mri_aparc2aseg —s <sub1> --labelwm --annot lobesfile 3. mri_segstats --seg mri/lobesfile+aseg.mgz --sum wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject <sub1> --surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt —etiv Now, I don’t know how to get the volumes or which LUT table to use in the overlay. Please correct me if I used the correct LUT file in --ctab. Your guidance would be highly appreciated. Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.
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